Natural Product: NPC7092

Natural Product IDNPC7092
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 BBOCDRLDMQHWJP-WOUKDFQISA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 96124
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0000479] Purine nucleosides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey BBOCDRLDMQHWJP-WOUKDFQISA-N
Standard InCHI InChI=1S/C12H17N5O5/c18-2-1-13-10-7-11(15-4-14-10)17(5-16-7)12-9(21)8(20)6(3-19)22-12/h4-6,8-9,12,18-21H,1-3H2,(H,13,14,15)/t6-,8-,9-,12-/m1/s1
SMILES C(CO)Nc1c2c(ncn1)n(cn2)[C@H]1[C@@H]([C@@H]([C@@H](CO)O1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   311.12 Volume:   278.828
?
Van der Waals volume.
Dense:   1.116 LogP:   -1.143
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.615
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.508
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   15.0
TPSA:   145.78
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.417 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.627 Fsp3:   0.583
MCE-18:   58.158
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.235 Fluc inhibitor:   0.028
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.035
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.054
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.042 Promiscuous compounds:   0.02

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.065 MDCK Permeability:   -5.269
Pgp-inhibitor:   0.0 Pgp-substrate:   0.381
PAMPA:   0.981
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.902
20% Bioavailability (F20%):   0.217 30% Bioavailability (F30%):   0.946
50% Bioavailability (F50%):   0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.199 MRP1:   0.155
Plasma Protein Binding (PPB):   46.443% Volume Distribution (VD):   -0.279
Fu: 52.845%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.997
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.051
BSEP inhibitor:   0.007

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.103 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.166
HLM stability:   0.005
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  7.383 Half-life (T1/2):  2.098

ADMET: Toxicity

hERG Blockers:  0.034 hERG Blockers (10um):  0.086
Human Hepatotoxicity (H-HT):  0.659 Drug-induced Liver Injury (DILI):  0.852
AMES Toxicity:  0.874 Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.021 Skin Sensitization:  0.996
Carcinogencity:  0.639 Eye Corrosion:  0.0
Eye Irritation:  0.505 Respiratory Toxicity:  0.367
Drug-induced Neurotoxicity:  0.523 Ototoxicity:  0.868
Hematotoxicity:  0.576 Drug-induced Nephrotoxicity:  0.81
Genotoxicity:  0.957 RPMI-8226 Immunitoxicity:  0.084
A549 Cytotoxicity:  0.092 Hek293 Cytotoxicity:  0.098
BCF:   0.083
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   1.896
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.547
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.601
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO27451 Ophiocordyceps sinensis Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27451 Ophiocordyceps sinensis Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27451 Ophiocordyceps sinensis Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27451 Ophiocordyceps sinensis Species Ophiocordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC7092 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7833 Intermediate Similarity NPC239737
0.7321 Intermediate Similarity NPC156461
0.7321 Intermediate Similarity NPC107374
0.7321 Intermediate Similarity NPC600382
0.7321 Intermediate Similarity NPC612067
0.6774 Remote Similarity NPC605318
0.6618 Remote Similarity NPC250178
0.6102 Remote Similarity NPC317821
0.5938 Remote Similarity NPC136349
0.5938 Remote Similarity NPC219313
0.5857 Remote Similarity NPC195140
0.5738 Remote Similarity NPC54320
0.5574 Remote Similarity NPC207633
0.5556 Remote Similarity NPC229974
0.5556 Remote Similarity NPC609036
0.5484 Remote Similarity NPC485738
0.5469 Remote Similarity NPC164665
0.5429 Remote Similarity NPC328479
0.5385 Remote Similarity NPC269827
0.5385 Remote Similarity NPC189068
0.5312 Remote Similarity NPC608634
0.5286 Remote Similarity NPC185991
0.5286 Remote Similarity NPC321814
0.5231 Remote Similarity NPC609472
0.5079 Remote Similarity NPC320818
0.5077 Remote Similarity NPC209525
0.5077 Remote Similarity NPC161659

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC7092 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.7581 Intermediate Similarity NPD1750 Clinical (unspecified phase)
0.7321 Intermediate Similarity NPD249 Phase 4
0.7321 Intermediate Similarity NPD250 Phase 4
0.7031 Intermediate Similarity NPD1369 Phase 2
0.6716 Remote Similarity NPD2965 Phase 2
0.5938 Remote Similarity NPD548 Clinical (unspecified phase)
0.5738 Remote Similarity NPD219 Phase 4
0.5738 Remote Similarity NPD220 Clinical (unspecified phase)
0.5526 Remote Similarity NPD2624 Phase 2
0.5385 Remote Similarity NPD195 Approved
0.5325 Remote Similarity NPD1732 Phase 3
0.5286 Remote Similarity NPD283 Phase 4
0.5231 Remote Similarity NPD186 Phase 1
0.5139 Remote Similarity NPD4171 Clinical (unspecified phase)
0.5122 Remote Similarity NPD2876 Phase 3
0.5122 Remote Similarity NPD2877 Clinical (unspecified phase)
0.5119 Remote Similarity NPD4495 Phase 1
0.5072 Remote Similarity NPD216 Approved

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data